FundingZiheng Yang is supported by a Biotechnological and Biological Sciences Research Council Grant. The infrastructure of the Anthropological Genetics Lab of M.E.S. at Hunter College (M.E.S.) was supported by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH).

Citations[C1] Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data. Richard D. Wilkinson, Michael E. Steiper, Christophe Soligo, Robert D. Martin, Ziheng Yang and Simon Tavaré. Systematic Biology 2010; ePub ahead of print. doi:10.1093/sysbio/syq054
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Abstract

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth–death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.

Keywords: approximate bayesian computation, molecular phylogeny, palaeontological data, primate divergence.

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[C2] A new hominid from the Upper Miocene of Chad, Central Africa. Michel Brunet, Franck Guy, David Pilbeam, Hassane Taisso Mackaye, Andossa Likius, Djimdoumalbaye Ahounta, Alain Beauvilain, Cécile Blondel, Hervé Bocherens, Jean-Renaud Boisserie, Louis De Bonis, Yves Coppens, Jean Dejax, Christiane Denys, Philippe Duringer, Véra Eisenmann, Gongdibé Fanone, Pierre Fronty, Denis Geraads, Thomas Lehmann, Fabrice Lihoreau, Antoine Louchart, Adoum Mahamat, Gildas Merceron, Guy Mouchelin, Olga Otero, Pablo Pelaez Campomanes, Marcia Ponce De Leon, Jean-Claude Rage, Michel Sapanet, Mathieu Schuster, Jean Sudre, Pascal Tassy, Xavier Valentin, Patrick Vignaud, Laurent Viriot, Antoine Zazzo and Christoph Zollikofer. Nature 2002; 418: 145-151. doi:10.1038/nature00879
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Abstract

The search for the earliest fossil evidence of the human lineage has been concentrated in East Africa. Here we report the discovery of six hominid specimens from Chad, central Africa, 2,500 km from the East African Rift Valley. The fossils include a nearly complete cranium and fragmentary lower jaws. The associated fauna suggest the fossils are between 6 and 7 million years old. The fossils display a unique mosaic of primitive and derived characters, and constitute a new genus and species of hominid. The distance from the Rift Valley, and the great antiquity of the fossils, suggest that the earliest members of the hominid clade were more widely distributed than has been thought, and that the divergence between the human and chimpanzee lineages was earlier than indicated by most molecular studies.

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[C3] Using the fossil record to estimate the age of the last common ancestor of extant primates. Simon Tavaré, Charles R. Marshall, Oliver Will, Christophe Soligo and Robert D. Martin. Nature 2002; 416: 726-729. doi:10.1038/416726a.

Abstract

Divergence times estimated from molecular data often considerably predate the earliest known fossil representatives of the groups studied. For the order Primates, molecular data calibrated with various external fossil dates uniformly suggest a mid-Cretaceous divergence from other placental mammals, some 90 million years (Myr) ago, whereas the oldest known fossil primates are from the basal Eocene epoch (54–55 Myr ago). The common ancestor of primates should be earlier than the oldest known fossils, but adequate quantification is needed to interpret possible discrepancies between molecular and palaeontological estimates. Here we present a new statistical method, based on an estimate of species preservation derived from a model of the diversification pattern, that suggests a Cretaceous last common ancestor of primates, approximately 81.5 Myr ago, close to the initial divergence time inferred from molecular data. It also suggests that no more than 7% of all primate species that have ever existed are known from fossils. The approach unites all the available palaeontological methods of timing evolutionary events: the fossil record, extant species and clade diversification models.